Installation guide: step by step

This document will guide you through the installation steps of the softwares needed for the hands-on sessions.
The steps are self-explainable, please perform all the installation steps in the menu on the left, prior to the workshop.

Don’t worry about your operating system. We have written installation options for Windows, Mac, and Linux.

Estimated time needed for this installation: 30 min - 1 hour

After finishing this guide, you have a working installation of:
- RStudio Desktop 1.4.1106 and >R4.0, and packages
- Python, Julia, manta, anuran, FLASHWEAVE
- Circos

Let’s get started!

Installation of Rstudio and R

R and RStudio are the basic programs used in this course. If you have already an R-version installed, take a moment to check if you are running the same version, R4.0.4. Our install will not mess up previous installed R-instances. So we recommend you to follow the R installation steps.

  1. For windows, you need RStudio for windows, and R-version 4.0.4 for windows. For Mac, you can download RStudio for Mac and R-version 4.0.4 for Mac. For Linux, e.g. Ubuntu 20.04, follow these instructions. If you have an account on the Flemish supercomputer and need help to Run R from there, mail me: . For other OS, read here. Execute the RStudio.exe and also the R4.0.4.exe, using the default settings.
    Tip: Choose language in English, if you want us to help understand error messages :-)

  2. Make a folder called MDAW e.g. in C:/Users/yourname/Documents. In this folder, place the RMDAW.zip file provided to you via google drive (folder R), and Unzip it.

  3. Go to the MDAW folder that you created in step 2. Double click on the MDAW.Rproj, it will open in Rstudio. Click file, open file, and navigate to your MDAW folder, and open the file 1.Initialise.R. In RStudio, please first check if you are using R 4.0.4 version. For this click, Tools > Global Options > and check which version is loaded under ‘R version’, select the 4.0.4 version if not already there. Click Apply, Ok. Now you are ready to run 1.initialise.R.
    Follow the instructions in the 1.Initialise.R file and execute all steps.
    The last command renv:restore can take 1 hour because it will auto-install all packages needed for the workshop, in the meantime you can watch this 15 min video to learn the basics of R, what is the console etc. and get familiar with the commands setwd and getwd().

  4. All done for Rstudio and R! You can proceed with the installation of the softwares for Tutorial4 and 5.

Installation of Circos (Tutorial 4)

With Circos you can visualise the correlations between microbiome data, transcriptomics data and various metadata such as metabolomics data-sets.

Sneak preview (credits Rossella Alfano):

Installation option 1: “hard way”

1)Download Circos
2)Install Circos

Installation option 2: Virtualbox
If the above didn’t work, follow the virtualbox installation instructions in which circos was pre-installed.

Installation of Julia, python (Tutorial 5)

For the network analyses Tutorial5 by Sam Röttjers, you need to install the following softwares.

Installation option 1: “hard way”

1)Install FlashWeave (and Julia)

2)Install Python 3

3)Install PyCharm or another Python editor of choice

4)Install manta

5)Install anuran

Installation option 2: Virtualbox
If you have downloaded and installed the virtualbox (VB) for the installation of circos, then you are good to go because in the VB all the softwares are pre-installed, also python, anuran. You can run the small test for manta, as explained.

Preparation for PEMA (Tutorial 7)

PEMA is a Pipeline for Environmental DNA Metabarcoding Analysis of the 16S ribosomal RNA (bacteria), ITS (fungi), COI and 18S (eukaryotes) marker genes. It is an automated workflow to go from raw reads to an OTU-table, and to perform downstream R (phyloseq) analyses.

Sneak preview (credits Haris Zafeiropoulus):

Although PEMA can be run on a simple PC (via Docker install), it is much more suited to be run on a High Performance Computing environment (server, cluster).

If you have a cluster available, you may want to install it, following these installation instructions.

If you have a simple pc, laptop, you are still able to run this pipeline via the Flemish supercomputer center. Because the vSC is highly secured, We will be using the free shell environment SDF to submit your job to our server (with basically Haris and me as the border controls :-)). So you will get your personal access key for SDF to learn to work in shell.

To do
Windows user:
- install PuTTY. It is a free SSH client to connect to the server.
- install FileZilla. FileZilla will be used to transfer files between your computer, and the server.

MAC-user:
- use Terminal.App to connect to the server
- install FileZilla for mac for file transfer.

Linux-user:
- You can connect to the server by using ssh in the terminal
- You can transfer files using command lines, or with FileZilla for Linux.

How to setup FileZilla
- Open FileZilla
- Click File > Site Manager
- Under the tab ‘General’ on the right, choose as protocol: SFTP - SSH File Transfer Protocol
- as host, type: tty.sdf.org, you can leave the port blank
- Logon Type: Normal
- User: your user name that you get from us
- Password: your password you get from us
- connect and then you are connected to the server. On the left is your pc with files, on the right the server, where you can transfer files too.

How to setup PuTTy
- Under Host Name, fill in: tty.sdf.org, leave the port as default
- Connection type should be SSH
- You can save this, by typing in Saved Sessions: SDF, press save
- Select SDF, and click open to launch the shell
- In the shell, after login as: give in your username
- Then it will ask for your password: copy your password from the email, and just press right mouse click in the shell to paste your password (you don’t see your password). But press enter.
- If all worked: you should see, Explore and Enjoy!

You are all done! Ready to follow Tutorial#7.

All done!

If you have installation problems or you just want a brief Q&A, you can schedule a one-on-one meeting in gather-town from April 12. You can mail me () to find an appropriate time-slot.